ProBiS is a computer software which allows prediction of binding sites and their corresponding ligands for a given protein structure. Initially ProBiS was developed as a ProBiS algorithm by Janez Konc and Dušanka Janežič in 2010[1] and is now available as ProBiS server, ProBiS CHARMMing server, ProBiS algorithm and ProBiS plugin. The name ProBiS originates from the purpose of the software itself, that is to predict for a given Protein structure Binding Sites and their corresponding ligands.
ProBiS software started as ProBiS algorithm that detects structurally similar sites on protein surfaces by local surface structure alignment using a fast maximum clique algorithm. The ProBiS algorithm was followed by ProBiS server which provides access to the program ProBiS that detects protein binding sites based on local structural alignments. There are two ProBiS servers available, ProBiS server and ProBiS CHARMMing server. The latter connects ProBiS and CHARMMing servers into one functional unit that enables prediction of protein−ligand complexes and allows for their geometry optimization and interaction energy calculation. The ProBiS CHARMMing server with these additional functions can only be used at National Institutes of Health, USA. Otherwise it acts as a regular ProBiS server. Additionally a ProBiS PyMOL plugin and ProBiS UCSF Chimera plugin have been made. Both plugins are connected via the internet to a newly prepared database of pre-calculated binding site comparisons to allow fast prediction of binding sites in existing proteins from the Protein Data Bank. They enable viewing of predicted binding sites and ligands poses in three-dimensional graphics.
Protein building sites toolsedit
An example output of the ProBiS software for detecting structurally similar binding sites.An example output of the ProBiS software for pairwise alignment of two proteins.
Detect structurally similar binding sites
This tool takes as an input a query protein or a binding site. The ProBiS algorithm structurally compares the query independently of sequence or fold with a database of non-redundant protein structures. The output of this tool are a 3D query protein colored by degrees of structural conservation from blue (unconserved) to red (structurally conserved) in Jmol viewer and a table of similar proteins.
Pairwise local structural alignment
This tool takes as an input two proteins or binding sites. The ProBiS algorithm compares structures based on geometry as well as physicochemical properties and returns their local structural alignment.
ProBiS web server RESTful Web Services
The ProBiS web server features RESTful (Representational State Transfer) web services to make the binding site similarities and local pairwise alignments for any PDB protein structure easily accessible from any script.
ProBiS-Database access
ProBiS-Database can be accessed directly from ProBiS (CHARMMing) server, ProBiS-Database widget, which can be included in any web page to provide access to the ProBiS-Database, or RESTful Web Services, which make ProBiS-Database easily accessible from any script.
Historyedit
ProBiS algorithm for detection of structurally similar protein binding sites by local structural alignment (March 2010)[1]
ProBiS: A web server for detection of structurally similar protein binding sites (February 2010)[2]
ProBiS-Database: Precalculated Binding Site Similarities and Local Pairwise Alignments of Pdb Structures (December 2011)[3]
ProBiS - 2012: Web server and web services for detection of structurally similar binding sites in proteins (February 2012)[4]
Parallel-ProBiS: Fast Parallel Algorithm for Local Structural Comparison of Protein Structures and Binding Sites (March 2012)[5]
ProBiS-ligands: a web server for prediction of ligands by examination of protein binding sites (February 2014)[6]
ProBiS-Charmming: Web Interface for Prediction and Optimization of Ligands in Protein Binding Sites (August 2015)[7]
Referencesedit
^ abJanez Konc; Dušanka Janežič (2010). "ProBiS algorithm for detection of structurally similar protein binding sites by local structural alignment". Bioinformatics. 26 (9): 1160–1168. doi:10.1093/bioinformatics/btq100. PMC2859123. PMID 20305268.
^Janez Konc; Dušanka Janežič (2010). "ProBiS: A web server for detection of structurally similar protein binding sites". Nucleic Acids Research. 38 (Web Server issue): W436–W440. doi:10.1093/nar/gkq479. PMC2896105. PMID 20504855.
^Tomo Česnik; Joanna Trykowska Konc; Matej Penca; Dušanka Janežič (2012). "ProBiS-Database: Precalculated Binding Site Similarities and Local Pairwise Alignments of Pdb Structures". Journal of Chemical Information and Modeling. 52 (2): 604–612. doi:10.1021/ci2005687. PMC3287116. PMID 22268964.
^Janez Konc; Dušanka Janežič (2012). "ProBiS - 2012: Web server and web services for detection of structurally similar binding sites in proteins" (PDF). Nucleic Acids Research. 40 (Web Server issue): W214–21. doi:10.1093/nar/gks435. PMC3394329. PMID 22600737.
^Janez Konc; Matjaz Depolli; Roman Trobec; Kati Rozman; Dušanka Janežič (2012). "Parallel-ProBiS: Fast Parallel Algorithm for Local Structural Comparison of Protein Structures and Binding Sites" (PDF). Journal of Computational Chemistry. 33 (27): 2199–2203. doi:10.1002/jcc.23048. PMID 22718529. S2CID 12067419.
^Janez Konc; Dušanka Janežič (2014). "ProBiS-ligands: a web server for prediction of ligands by examination of protein binding sites". Nucleic Acids Research. 42 (Web Server issue): W215–20. doi:10.1093/nar/gku460. PMC4086080. PMID 24861616.
^Janez Konc; Benjamin T. Miller; Tanja Štular; Samo Lešnik; H. Lee Woodcock; Bernard R. Brooks; Dušanka Janežič (2015). "ProBiS-Charmming: Web Interface for Prediction and Optimization of Ligands in Protein Binding Sites". Journal of Chemical Information and Modeling. 55 (11): 2308–2314. doi:10.1021/acs.jcim.5b00534. PMC8725999. PMID 26509288.
External linksedit
ProBiS server
January 01, 1970
probis, computer, software, which, allows, prediction, binding, sites, their, corresponding, ligands, given, protein, structure, initially, developed, algorithm, janez, konc, dušanka, janežič, 2010, available, server, charmming, server, algorithm, plugin, name. ProBiS is a computer software which allows prediction of binding sites and their corresponding ligands for a given protein structure Initially ProBiS was developed as a ProBiS algorithm by Janez Konc and Dusanka Janezic in 2010 1 and is now available as ProBiS server ProBiS CHARMMing server ProBiS algorithm and ProBiS plugin The name ProBiS originates from the purpose of the software itself that is to predict for a given Protein structure Binding Sites and their corresponding ligands ProBiSDeveloper s Insilab National Institute of Chemistry Slovenia Initial release2010 14 years ago 2010 Written inC JavaScript PHPOperating systemUnix like WindowsTypeWeb server plugin algorithm databaseWebsiteprobis wbr cmm wbr ki wbr si Contents 1 Description 2 Protein building sites tools 3 History 4 References 5 External linksDescription editProBiS software started as ProBiS algorithm that detects structurally similar sites on protein surfaces by local surface structure alignment using a fast maximum clique algorithm The ProBiS algorithm was followed by ProBiS server which provides access to the program ProBiS that detects protein binding sites based on local structural alignments There are two ProBiS servers available ProBiS server and ProBiS CHARMMing server The latter connects ProBiS and CHARMMing servers into one functional unit that enables prediction of protein ligand complexes and allows for their geometry optimization and interaction energy calculation The ProBiS CHARMMing server with these additional functions can only be used at National Institutes of Health USA Otherwise it acts as a regular ProBiS server Additionally a ProBiS PyMOL plugin and ProBiS UCSF Chimera plugin have been made Both plugins are connected via the internet to a newly prepared database of pre calculated binding site comparisons to allow fast prediction of binding sites in existing proteins from the Protein Data Bank They enable viewing of predicted binding sites and ligands poses in three dimensional graphics Protein building sites tools edit nbsp An example output of the ProBiS software for detecting structurally similar binding sites nbsp An example output of the ProBiS software for pairwise alignment of two proteins Detect structurally similar binding sites This tool takes as an input a query protein or a binding site The ProBiS algorithm structurally compares the query independently of sequence or fold with a database of non redundant protein structures The output of this tool are a 3D query protein colored by degrees of structural conservation from blue unconserved to red structurally conserved in Jmol viewer and a table of similar proteins Pairwise local structural alignment This tool takes as an input two proteins or binding sites The ProBiS algorithm compares structures based on geometry as well as physicochemical properties and returns their local structural alignment ProBiS web server RESTful Web Services The ProBiS web server features RESTful Representational State Transfer web services to make the binding site similarities and local pairwise alignments for any PDB protein structure easily accessible from any script ProBiS Database access ProBiS Database can be accessed directly from ProBiS CHARMMing server ProBiS Database widget which can be included in any web page to provide access to the ProBiS Database or RESTful Web Services which make ProBiS Database easily accessible from any script History editProBiS algorithm for detection of structurally similar protein binding sites by local structural alignment March 2010 1 ProBiS A web server for detection of structurally similar protein binding sites February 2010 2 ProBiS Database Precalculated Binding Site Similarities and Local Pairwise Alignments of Pdb Structures December 2011 3 ProBiS 2012 Web server and web services for detection of structurally similar binding sites in proteins February 2012 4 Parallel ProBiS Fast Parallel Algorithm for Local Structural Comparison of Protein Structures and Binding Sites March 2012 5 ProBiS ligands a web server for prediction of ligands by examination of protein binding sites February 2014 6 ProBiS Charmming Web Interface for Prediction and Optimization of Ligands in Protein Binding Sites August 2015 7 References edit a b Janez Konc Dusanka Janezic 2010 ProBiS algorithm for detection of structurally similar protein binding sites by local structural alignment Bioinformatics 26 9 1160 1168 doi 10 1093 bioinformatics btq100 PMC 2859123 PMID 20305268 Janez Konc Dusanka Janezic 2010 ProBiS A web server for detection of structurally similar protein binding sites Nucleic Acids Research 38 Web Server issue W436 W440 doi 10 1093 nar gkq479 PMC 2896105 PMID 20504855 Tomo Cesnik Joanna Trykowska Konc Matej Penca Dusanka Janezic 2012 ProBiS Database Precalculated Binding Site Similarities and Local Pairwise Alignments of Pdb Structures Journal of Chemical Information and Modeling 52 2 604 612 doi 10 1021 ci2005687 PMC 3287116 PMID 22268964 Janez Konc Dusanka Janezic 2012 ProBiS 2012 Web server and web services for detection of structurally similar binding sites in proteins PDF Nucleic Acids Research 40 Web Server issue W214 21 doi 10 1093 nar gks435 PMC 3394329 PMID 22600737 Janez Konc Matjaz Depolli Roman Trobec Kati Rozman Dusanka Janezic 2012 Parallel ProBiS Fast Parallel Algorithm for Local Structural Comparison of Protein Structures and Binding Sites PDF Journal of Computational Chemistry 33 27 2199 2203 doi 10 1002 jcc 23048 PMID 22718529 S2CID 12067419 Janez Konc Dusanka Janezic 2014 ProBiS ligands a web server for prediction of ligands by examination of protein binding sites Nucleic Acids Research 42 Web Server issue W215 20 doi 10 1093 nar gku460 PMC 4086080 PMID 24861616 Janez Konc Benjamin T Miller Tanja Stular Samo Lesnik H Lee Woodcock Bernard R Brooks Dusanka Janezic 2015 ProBiS Charmming Web Interface for Prediction and Optimization of Ligands in Protein Binding Sites Journal of Chemical Information and Modeling 55 11 2308 2314 doi 10 1021 acs jcim 5b00534 PMC 8725999 PMID 26509288 External links editProBiS server Retrieved from https en wikipedia org w index php title ProBiS amp oldid 1162525838, wikipedia, wiki, book, books, library,
